protocols::medal::MedalMover Class Reference

#include <MedalMover.hh>

Inheritance diagram for protocols::medal::MedalMover:

Collaboration diagram for protocols::medal::MedalMover:

List of all members.

Public Member Functions
	MedalMover ()
void	apply (core::pose::Pose &pose)
std::string	get_name () const
	Each derived class must specify its name. The class name.
protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected.
protocols::moves::MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function _should_ be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).
Protected Types
typedef utility::vector1< double >	Probabilities
Protected Member Functions
void	do_loop_closure (core::pose::Pose *pose) const
	Closes chainbreaks in <pose>
void	compute_per_residue_probabilities (const unsigned num_residues, const core::sequence::SequenceAlignment &alignment, const protocols::loops::Loops &chunks, const core::kinematics::FoldTree &tree, const core::fragment::FragSet &fragments, Probabilities *probs) const
	Computes per-residue sampling probabilities.
void	decompose_structure (const core::pose::Pose &pose, protocols::loops::LoopsOP &chunks) const
	Partitions the structure into non-overlapping chunks.
protocols::moves::MoverOP	create_fragment_mover (core::pose::PoseOP native, core::scoring::ScoreFunctionOP score, core::fragment::FragSetOP fragments, const Probabilities &probs, const std::string &policy, unsigned library_size) const
	Configures a mover for biased fragment insertion.
protocols::moves::MoverOP	create_fragment_and_rigid_mover (const core::pose::Pose &pose, core::pose::PoseOP native, core::scoring::ScoreFunctionOP score, core::fragment::FragSetOP fragments, const Probabilities &probs, const std::string &policy, unsigned library_size) const
	Configures a mover for alternating biased fragment insertion and rigid body moves.
protocols::moves::MoverOP	create_small_mover (core::pose::PoseOP native, core::scoring::ScoreFunctionOP score) const
	Configures a mover for performing alternating small and shear moves.
core::scoring::ScoreFunctionOP	score_function () const
	Configures a basic score functions which callers can then specialize.
Protected Attributes
core::fragment::FragSetOP	fragments_sm_
core::fragment::FragSetOP	fragments_lg_

---

Member Typedef Documentation

typedef utility::vector1<double> protocols::medal::MedalMover::Probabilities [protected]

---

Constructor & Destructor Documentation

protocols::medal::MedalMover::MedalMover

(

)

References fragments_lg_, and fragments_sm_.

Referenced by clone(), and fresh_instance().

---

Member Function Documentation

void protocols::medal::MedalMover::apply

(

core::pose::Pose &

pose

)

[virtual]

Implements protocols::moves::Mover.

References core::scoring::constraints::add_constraints_from_cmdline_to_pose(), core::util::add_cutpoint_variants(), core::chemical::CENTROID, compute_per_residue_probabilities(), create_fragment_and_rigid_mover(), create_small_mover(), protocols::nonlocal::current_job(), decompose_structure(), do_loop_closure(), core::pose::Pose::fold_tree(), fragments_sm_, core::scoring::linear_chainbreak, core::scoring::constraints::linear_interpolate(), core::import_pose::pose_from_pdb(), core::util::remove_cutpoint_variants(), score_function(), protocols::nonlocal::StarTreeBuilder::set_up(), core::util::switch_to_residue_type_set(), core::pose::Pose::total_residue(), and protocols::medal::TR().

protocols::moves::MoverOP protocols::medal::MedalMover::clone

(

)

const [virtual]

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

References MedalMover().

void protocols::medal::MedalMover::compute_per_residue_probabilities	(	const unsigned	num_residues,
		const core::sequence::SequenceAlignment &	alignment,
		const protocols::loops::Loops &	chunks,
		const core::kinematics::FoldTree &	tree,
		const core::fragment::FragSet &	fragments,
		Probabilities *	probs
	)		const [protected]

Computes per-residue sampling probabilities.

References protocols::medal::alignment_probabilities(), protocols::medal::chunk_probabilities(), protocols::medal::cutpoint_probabilities(), protocols::medal::end_bias_probabilities(), protocols::medal::invalidate_residues_spanning_cuts(), core::fragment::FragSet::max_frag_length(), and protocols::medal::TR().

Referenced by apply().

protocols::moves::MoverOP protocols::medal::MedalMover::create_fragment_and_rigid_mover	(	const core::pose::Pose &	pose,
		core::pose::PoseOP	native,
		core::scoring::ScoreFunctionOP	score,
		core::fragment::FragSetOP	fragments,
		const Probabilities &	probs,
		const std::string &	policy,
		unsigned	library_size
	)		const [protected]

Configures a mover for alternating biased fragment insertion and rigid body moves.

References core::pose::Pose::fold_tree(), and protocols::medal::on_pose_accept().

Referenced by apply().

protocols::moves::MoverOP protocols::medal::MedalMover::create_fragment_mover	(	core::pose::PoseOP	native,
		core::scoring::ScoreFunctionOP	score,
		core::fragment::FragSetOP	fragments,
		const Probabilities &	probs,
		const std::string &	policy,
		unsigned	library_size
	)		const [protected]

Configures a mover for biased fragment insertion.

References protocols::medal::on_pose_accept().

protocols::moves::MoverOP protocols::medal::MedalMover::create_small_mover	(	core::pose::PoseOP	native,
		core::scoring::ScoreFunctionOP	score
	)		const [protected]

Configures a mover for performing alternating small and shear moves.

References protocols::medal::on_pose_accept().

Referenced by apply().

void protocols::medal::MedalMover::decompose_structure	(	const core::pose::Pose &	pose,
		protocols::loops::LoopsOP &	chunks
	)		const [protected]

Partitions the structure into non-overlapping chunks.

References protocols::nonlocal::chunks_by_CA_CA_distance().

Referenced by apply().

void protocols::medal::MedalMover::do_loop_closure

(

core::pose::Pose *

pose

)

const [protected]

Closes chainbreaks in <pose>

References core::pose::Pose::fold_tree(), fragments_sm_, protocols::comparative_modeling::LoopRelaxMover::remodel(), and core::pose::Pose::total_residue().

Referenced by apply().

protocols::moves::MoverOP protocols::medal::MedalMover::fresh_instance

(

)

const [virtual]

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function _should_ be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

References MedalMover().

std::string protocols::medal::MedalMover::get_name

(

)

const [virtual]

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

core::scoring::ScoreFunctionOP protocols::medal::MedalMover::score_function

(

)

const [protected]

Configures a basic score functions which callers can then specialize.

Configures the score function used during the simulation. Precedence: 1. User-specified patch file (i.e. -rigid:patch) 2. User-specified options (e.g. -jumps:increase_chainbreak) 3. Default values

References core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep(), core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, and core::scoring::linear_chainbreak.

Referenced by apply().

---

Member Data Documentation

core::fragment::FragSetOP protocols::medal::MedalMover::fragments_lg_ [protected]

Referenced by MedalMover().

core::fragment::FragSetOP protocols::medal::MedalMover::fragments_sm_ [protected]

Referenced by apply(), do_loop_closure(), and MedalMover().

---

The documentation for this class was generated from the following files:

• src/protocols/medal/MedalMover.hh
• src/protocols/medal/MedalMover.cc